Vertical habitat preferences shape the fish gut microbiota in a shallow lake
Understanding the interactions between fish gut microbiota and the aquatic environment is a key issue for understanding aquatic microorganisms. Environmental microorganisms enter fish intestines through feeding, and the amount of invasion varies due to different feeding habits. Traditional fish feed...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1341303/full |
| _version_ | 1797257827769647104 |
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| author | Bowei Zhang Bowei Zhang Jiaman Xiao Jiaman Xiao Hongyan Liu Hongyan Liu Dongdong Zhai Dongdong Zhai Ying Wang Ying Wang Shujun Liu Shujun Liu Fei Xiong Fei Xiong Ming Xia Ming Xia |
| author_facet | Bowei Zhang Bowei Zhang Jiaman Xiao Jiaman Xiao Hongyan Liu Hongyan Liu Dongdong Zhai Dongdong Zhai Ying Wang Ying Wang Shujun Liu Shujun Liu Fei Xiong Fei Xiong Ming Xia Ming Xia |
| author_sort | Bowei Zhang |
| collection | DOAJ |
| description | Understanding the interactions between fish gut microbiota and the aquatic environment is a key issue for understanding aquatic microorganisms. Environmental microorganisms enter fish intestines through feeding, and the amount of invasion varies due to different feeding habits. Traditional fish feeding habitat preferences are determined by fish morphology or behavior. However, little is known about how the feeding behavior of fish relative to the vertical structure in a shallow lake influences gut microbiota. In our study, we used nitrogen isotopes to measure the trophic levels of fish. Then high-throughput sequencing was used to describe the composition of environmental microbiota and fish gut microbiota, and FEAST (fast expectation-maximization for microbial source tracking) method was used to trace the source of fish gut microbiota. We investigated the microbial diversity of fish guts and their habitats in Lake Sanjiao and verified that the sediments indeed played an important role in the assembly of fish gut microbiota. Then, the FEAST analysis indicated that microbiota in water and sediments acted as the primary sources in half of the fish gut microbiota respectively. Furthermore, we classified the vertical habitat preferences using microbial data and significant differences in both composition and function of fish gut microbiota were observed between groups with distinct habitat preferences. The performance of supervised and unsupervised machine learning in classifying fish gut microbiota by habitat preferences actually exceeded classification by fish species taxonomy and fish trophic level. Finally, we described the stability of fish co-occurrence networks with different habitat preferences. Interestingly, the co-occurrence network seemed more stable in pelagic fish than in benthic fish. Our results show that the preferences of fish in the vertical structure of habitat was the main factor affecting their gut microbiota. We advocated the use of microbial interactions between fish gut and their surrounding environment to reflect fish preferences in vertical habitat structure. This approach not only offers a novel perspective for understanding the interactions between fish gut microbiota and environmental factors, but also provides new methods and ideas for studying fish habitat selection in aquatic ecosystems. |
| first_indexed | 2024-04-24T22:43:50Z |
| format | Article |
| id | doaj.art-a041f7a0a73f4e1f9e68436b585b0e36 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-24T22:43:50Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-a041f7a0a73f4e1f9e68436b585b0e362024-03-18T17:20:29ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2024-03-011510.3389/fmicb.2024.13413031341303Vertical habitat preferences shape the fish gut microbiota in a shallow lakeBowei Zhang0Bowei Zhang1Jiaman Xiao2Jiaman Xiao3Hongyan Liu4Hongyan Liu5Dongdong Zhai6Dongdong Zhai7Ying Wang8Ying Wang9Shujun Liu10Shujun Liu11Fei Xiong12Fei Xiong13Ming Xia14Ming Xia15Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaHubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaHubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaHubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaHubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaHubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaHubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaHubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, ChinaHubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, ChinaUnderstanding the interactions between fish gut microbiota and the aquatic environment is a key issue for understanding aquatic microorganisms. Environmental microorganisms enter fish intestines through feeding, and the amount of invasion varies due to different feeding habits. Traditional fish feeding habitat preferences are determined by fish morphology or behavior. However, little is known about how the feeding behavior of fish relative to the vertical structure in a shallow lake influences gut microbiota. In our study, we used nitrogen isotopes to measure the trophic levels of fish. Then high-throughput sequencing was used to describe the composition of environmental microbiota and fish gut microbiota, and FEAST (fast expectation-maximization for microbial source tracking) method was used to trace the source of fish gut microbiota. We investigated the microbial diversity of fish guts and their habitats in Lake Sanjiao and verified that the sediments indeed played an important role in the assembly of fish gut microbiota. Then, the FEAST analysis indicated that microbiota in water and sediments acted as the primary sources in half of the fish gut microbiota respectively. Furthermore, we classified the vertical habitat preferences using microbial data and significant differences in both composition and function of fish gut microbiota were observed between groups with distinct habitat preferences. The performance of supervised and unsupervised machine learning in classifying fish gut microbiota by habitat preferences actually exceeded classification by fish species taxonomy and fish trophic level. Finally, we described the stability of fish co-occurrence networks with different habitat preferences. Interestingly, the co-occurrence network seemed more stable in pelagic fish than in benthic fish. Our results show that the preferences of fish in the vertical structure of habitat was the main factor affecting their gut microbiota. We advocated the use of microbial interactions between fish gut and their surrounding environment to reflect fish preferences in vertical habitat structure. This approach not only offers a novel perspective for understanding the interactions between fish gut microbiota and environmental factors, but also provides new methods and ideas for studying fish habitat selection in aquatic ecosystems.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1341303/fullfeeding habitat preferencetrophic levellake ecosystemmicrobial community coalescencefish gut microbiota |
| spellingShingle | Bowei Zhang Bowei Zhang Jiaman Xiao Jiaman Xiao Hongyan Liu Hongyan Liu Dongdong Zhai Dongdong Zhai Ying Wang Ying Wang Shujun Liu Shujun Liu Fei Xiong Fei Xiong Ming Xia Ming Xia Vertical habitat preferences shape the fish gut microbiota in a shallow lake Frontiers in Microbiology feeding habitat preference trophic level lake ecosystem microbial community coalescence fish gut microbiota |
| title | Vertical habitat preferences shape the fish gut microbiota in a shallow lake |
| title_full | Vertical habitat preferences shape the fish gut microbiota in a shallow lake |
| title_fullStr | Vertical habitat preferences shape the fish gut microbiota in a shallow lake |
| title_full_unstemmed | Vertical habitat preferences shape the fish gut microbiota in a shallow lake |
| title_short | Vertical habitat preferences shape the fish gut microbiota in a shallow lake |
| title_sort | vertical habitat preferences shape the fish gut microbiota in a shallow lake |
| topic | feeding habitat preference trophic level lake ecosystem microbial community coalescence fish gut microbiota |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1341303/full |
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